It does first check if there is anything on the agency. And submits anything it finds.
And only after this it will start the countdown for the next check.
If you need to upload new files you need to select the desired agencies with the left checkboxes and click Upload now button.
The submission is the second step that does fill custom metadata fields on the agency (releases, categories, etc.) and send images to the review.
It is not possible to submit images that weren't uploaded or are not yet appeared at the agency website.